I have a similar question about the "job waiting to run" status: I uploaded my files locally from my computer using the Get Data>Upload file from computer options. The uploading according to the pop-up box was successful, as indicated by the full green bar ("100%" and check mark), and was added to my history list. However, the listed file is highlighted gray and has the "job waiting to run" status, unlike my previously uploaded files. What is going on? Normally, the uploading in the pop-up window takes a while, today it was seemingly much faster... but is not tied up in my "history" box.

The job is probably queued and will fully load. Give it some time. Be sure to click on the history reload button (top of the history panel, double circle) to refresh the view - this will show the most current job status.

There is probably nothing to fix, upload has multiple steps - one of them is to physically move the file to Galaxy server but then there are others like metadata detection and sniffing of type etc. The extra steps are indicated by the dataset state - so you just have to wait for the extra steps to be finished.